Sequencing ServicesDeep Shotgun Metagenomic Sequencing


In shotgun metagenomics, whole DNA is extracted from a sample then exposed to random fragmentation prior to NGS. By taking an untargeted approach to sequencing whole DNA and avoiding primer-dependent, PCR Amplification like in amplicon sequencing services, one gains an exponential amount of data and advantages alongside it.

Deep Shotgun SequencingWhat are the advantages?

  • No amplification bias

  • Lower false-positive rates relative to amplicon sequencing

  • Higher-resolution (species, sub-species & strain-level) analysis

  • Multi-Kingdom Analysis – Bacteria, Viruses, Bacteriophages, Fungi & Protists

  • Characterization – Antimicrobial Resistance, Plasmids, Virulence Factors & Functional Genes

Deep shotgun sequencing sample zoomed in

Deep Shotgun SequencingIs Shotgun Metagenomics right for me?

Given the ability to provide not only very detailed information on taxonomy, but also the functional potential of a metagenome, this method is unparalleled for correlating with multi-omics, metadata and other study variables to unlock the microbiome.

Common applications include, but are not limited to:

  • Discovery research in human health & disease

  • Clinical sample analysis for primary or exploratory endpoints in pharmaceutical & nutritional studies

  • Biomarker discovery & patient stratification efforts in pharmaceutical drug development

  • Strain-tracking & epidemiology

  • Clinical Metagenomics & Infectious Disease Diagnostics

  • Donor & Recipient Screening in Fecal Microbiota Transfer (FMT) studies/treatment

  • Food Safety & Spoilage studies

  • Agricultural & Environmental Research

Deep Shotgun Human Sequencing Services & Solutions

The CosmosID team have extensive experience in supporting the design and execution of shotgun-based metagenomic sequencing projects for both industry and academia for a wide range of applications, using both human and non-human sample types.


Deep Shotgun SequencingSample Processing

CosmosID’s CLIA-certified, GCP compliant facility receives samples from all around the world. Whether you’re batch sending samples for a microbiome R&D project or coordinating with multiple clinical trial sites, your precious samples will be barcoded & accessioned into the CosmosID LIMS system for sample tracking and project management purposes.

CosmosID also offers validated DNA extraction protocols optimized for shotgun sequencing and based on sample type, resulting in minimal bias, optimum yield and purity for your most prioritized organisms.

Deep Shotgun SequencingLibrary Preparation & Sequencing

Once DNA QC metrics are established for received or generated DNA samples, these samples then undergo library preparation & QC prior to sequencing on a range of different instruments, depending on study question & client preference:

  • Illumina NextSeq 550

  • Illumina HiSeq4000

  • Illumina NovaSeq6000

  • ION Torrent S5 XL

In addition to this, CosmosID also offers a range of different sequencing depths from 6M to 100M reads with different run-type/flowcell options.

Deep Shotgun SequencingBioinformatics & Other Deliverables

In addition to sample processing & sequencing, CosmosID includes, as standard, access to the CosmosID -Hub where you can expect:

  • Industry-leading species & strain-level resolution of bacteria, viruses, bacteriophages, fungi & protists

  • Access to AMR & Virulence Analysis

  • Interactive and user-friendly charts & visualizations with access to comparative analysis features including heat maps, PCA plots, Alpha Diversity & Beta Diversity PCoA

  • Methods & QC data upon request – DNA QC, Library QC & fastQC

  • Fastq/Fasta file transfer via AWS s3 Bucket/Dropbox

Deep Shotgun SequencingTurnaround Time & Customer Service

Deadline coming up? CosmosID offers different turnaround time options as fast as 3-5 business days for shotgun sequencing & genome analysis. Simply let us know about any special requirements and we can tailor our complex genome shotgun sequencing services accordingly.

Once samples have arrived at the lab, our operations team will keep you updated on a weekly basis on the status of your study and the rapid and sensitive classification of your metagenomic sequences. Request a quote for expert human genome sequence research and analysis from the microbial community today!

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Deep Shotgun SequencingFrequently Asked Questions

When would you require deep vs. shallow shotgun?

This is largely dependant on your sample type and  study question, with as simplified overview shown in the table below:
How do CosmosID advise on sequencing depth?

We will consult on sequencing depth based upon three main criteria: 

  1. Specimen type – taking into account host DNA interference and microbial diversity 
  2. Desired information – whether you are interested in taxa and/or function  
  3. Purpose  – evaluating the sensitivity required for your main study question, be that low cost surveillance or discovery of novel features.
What is the sequencing depth range available for shotgun metagenomics?

A wide range of depths are readily available at CosmosID, from 3M to 100M total reads and beyond, if necessary, with exact specifications available upon request.